tbuckley/cabot-search huggingface dataset:
Can a Purposeful Walk Intervention with a Distance Goal Using an Activity Monitor Improve Individuals’ Daily Activity and Function Post Total Hip Replacement Surgery. A Randomized Pilot Trial
Authors: Shayan Bahadori, Jonathan Mark Williams, Sarah Collard, Ian Swain
Journal: Cyborg and Bionic Systems (2023)

Individuals have increasingly high expectations of return to activity following total hip replacement (THR) surgery. The current literature demonstrates marked improvements in pain following THR. However, there is limited evidence showing objective improvement in daily activity. This randomized pilot trial aimed to determine the effect of an intervention where outdoor walking distance is used as a goal to increase daily activity of older adults using a commercial activity monitor at 3 to 6 months post THR. Findings suggested that the participants in the intervention group had higher activity levels after THR, compared to those in the control group. The Cohen's effect sizes were larger for the changes in the gait, Hip Disability and Osteoarthritis Outcome Score, and Psychosocial Impact of Assistive Devices Scale data in the intervention group in contrast to the control group. However, further research with a larger sample size is required to provide tangible evidence on the significance of the effect of the purposeful walk compared to step count.
Comparative effectiveness of non-pharmacological interventions on sleep in individuals with chronic musculoskeletal pain: A systematic review with network meta-analysis
Authors: Jeremy R. Chang, Yuen Kwan Cheung, Saurab Sharma, Shirley X. Li, Rae RY. Tao, Janet Lok Chun Lee, Eliza R. Sun, Sabina M. Pinto, Zhixing Zhou, Howard Fong, Winnie WY. Chan, Kangyong Zheng, Dino Samartzis, Siu-Ngor Fu, Arnold YL. Wong
Journal: Sleep Medicine Reviews (2023)

This network meta-analysis aimed to estimate the comparative effectiveness of non-pharmacological interventions on sleep in individuals with chronic musculoskeletal pain. Seven databases were systematically searched up to February 2023. A random-effects network meta-analysis in a frequentist framework was performed to synthesize continuous data as standardized mean differences (SMD) along with a 95% confidence interval (95% CI). A total of 15,641 records were identified, and 107 randomized controlled trials involving 8,121 participants were included. Of 14 identified interventions, eight were significantly more effective than passive control in improving sleep quality at immediate post-intervention (SMDs = 0.67-0.74), with cognitive behavioral therapy (CBT) being the most effective treatment (SMD = 0.74, 95% CI: 0.45-1.03). Only CBT demonstrated sustained effects at short-term (SMD = 1.56; 95% CI: 0.62-2.49) and mid-term (SMD = 1.23; 95% CI: 0.44-2.03) follow-ups. Furthermore, CBT significantly improved subjective (SMD = 0.64; 95% CI: 0.25-1.03) and objective (SMD = 0.30; 95% CI: 0.01-0.59) sleep efficiency compared with passive control at immediate post-intervention. Our findings support CBT as the first-line treatment for improving sleep in individuals with chronic musculoskeletal pain, given its superior effectiveness across multiple sleep outcomes and its sustainable effects until mid-term follow-up. However, the certainty of evidence for these interventions in improving sleep quality was very low to low.
A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction
Authors: Farzaneh Esmaili, Mahdi Pourmirzaei, Shahin Ramazi, Seyedehsamaneh Shojaeilangari, Elham Yavari
Journal: Genomics Proteomics & Bioinformatics (2023)

Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The purpose of this review is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively review all related databases and introduce all steps regarding dataset creation, data preprocessing, and method evaluation in p-site prediction. Next, we investigate p-site prediction methods, which are divided into two computational groups: algorithmic and machine learning (ML). Additionally, it is shown that there are basically two main approaches for p-site prediction by ML: conventional and end-to-end deep learning methods, both of which are given an overview. Moreover, this review introduces the most important feature extraction techniques, which have mostly been used in p-site prediction. Finally, we create three test sets from new proteins related to the released version of the database of protein post-translational modifications (dbPTM) in 2022 based on general and human species. Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release, distinct from those in the dbPTM 2019 release, reveals their limitations. In other words, the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research papers.
Outdoor Ultrafine Particulate Matter and Risk of Lung Cancer in Southern California
Authors: Rena R. Jones, Jared A. Fisher, Sina Hasheminassab, Joel D. Kaufman, Neal D. Freedman, Mary H. Ward, Constantinos Sioutas, Roel Vermeulen, Gerard Hoek, Debra T. Silverman
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

Particulate matter ⩽2.5 μm in aerodynamic diameter (PM
Evidence-Based Care of Older Adults With Metastatic Colorectal Cancer: Insights From Landmark Clinical Trials
Authors: Dina Ioffe, Efrat Dotan
Journal: Journal of Clinical Oncology (2023)

The Oncology Grand Rounds series is designed to place original reports published in the Journal into clinical context. A case presentation is followed by a description of diagnostic and management challenges, a review of the relevant literature, and a summary of the authors' suggested management approaches. The goal of this series is to help readers better understand how to apply the results of key studies, including those published in Journal of Clinical Oncology, to patients seen in their own clinical practice.Colorectal cancer (CRC) is the second leading cause of cancer-related death in the United States with more than half of the patients diagnosed being older than 65 years, and an expected further increase in older adults (OA) diagnosed with this cancer in the coming years as the population ages. Prospective data guiding the management of older patients with metastatic CRC (mCRC) have been limited and treatment decisions for these patients are often guided by chronologic age, crude evaluation of performance status, and extrapolation from trials conducted in younger individuals. Recent evidence from randomized clinical trials specifically designed for OA supports treatment deintensification and dose modification to increase tolerability without compromising efficacy in older, frailer patients with mCRC. Additional studies support the incorporation of geriatric assessment (GA)-driven care to further improve the outcomes of OA with mCRC. Although the use of GA has not been validated in guiding specific treatment selection or modification for OA with mCRC, it provides a comprehensive and objective evaluation of a patient's functional status, comorbidities, risk of potential toxicities, effect on the quality of life, goals of care, and assists with personalizing therapy. With the increase in the number of OA we care for in our practices, it is time to stop extrapolating and define an evidence-based approach for this population that is based on data from prospective elderly specific clinical trials.
Sexual Health in Adolescents and Young Adults With Cancer
Authors: Brooke O. Cherven, Jenna Demedis, Natasha N. Frederick
Journal: Journal of Clinical Oncology (2023)

Sexual health (SH), an integral aspect of overall health and quality of life, can be negatively affected by cancer and cancer treatment. SH is influenced by biological, psychological, social, and cultural factors, and, for adolescents and young adults (AYAs), developmental factors. The AYA population (age 15-39 years) is diverse in terms of psychosexual development, interpersonal relationships, and varying levels of independence, resulting in unique SH needs for this population. AYAs with cancer are particularly vulnerable to unmet SH needs related to contraception and infection prevention, sexual function, body image, and romantic/sexual relationships. Sexual dysfunction during and after cancer treatment is reported by 30%-100% of AYA cancer survivors. Clinical guidelines recommend discussing SH and screening for dysfunction but currently lack specifics regarding psychosexual interventions and strategies for incorporating screening into clinical care. Research and clinical priorities include improved provider-AYA communication regarding SH, standardization of SH measures and screening tools, infrastructure to support the SH needs of AYAs across pediatric and adult clinical environments, and engagement of sexual and gender minority AYAs in research. As the field of SH in cancer evolves, interventions need to be tailored to the developmental needs that are unique to AYAs and address the multidimensional aspects of SH.
Elucidating the Benefit of Radiation Therapy in GI Cancers: Rethinking Trial End Points and Patient Selection
Authors: Nina N. Sanford, Theodore S. Hong, William A. Hall
Journal: Journal of Clinical Oncology (2023)

all modalities should be appropriately designed to evaluate the benefit of new regimens.We believe that RT improves outcomes that matter to patients.Refining end points based upon patient values and tailoring inclusion criteria in clinical trials of RT will help generate much needed evidence for our modality.
Long-term risk of arrhythmias in patients with inflammatory bowel disease: A population-based, sibling-controlled cohort study
Authors: Jiangwei Sun, Bjorn Roelstraete, Emma Svennberg, Jonas Halfvarson, Johan Sundström, Anders Forss, Ola Olén, Jonas F. Ludvigsson
Journal: PLoS Medicine (2023)

Although previous evidence has suggested an increased risk of cardiovascular disease (CVD) in patients with inflammatory bowel disease (IBD), its association with arrhythmias is inconclusive. In this study, we aimed to explore the long-term risk of arrhythmias in patients with IBD.Through a nationwide histopathology cohort, we identified patients with biopsy-confirmed IBD in Sweden during 1969 to 2017, including Crohn's disease (CD: n = 24,954; median age at diagnosis: 38.4 years; female: 52.2%), ulcerative colitis (UC: n = 46,856; 42.1 years; 46.3%), and IBD-unclassified (IBD-U: n = 12,067; 43.8 years; 49.6%), as well as their matched reference individuals and IBD-free full siblings. Outcomes included overall and specific arrhythmias (e.g., atrial fibrillation/flutter, bradyarrhythmias, other supraventricular arrhythmias, and ventricular arrhythmias/cardiac arrest). Flexible parametric survival models estimated hazard ratios (aHR) with 95% confidence intervals (95% CIs), after adjustment for birth year, sex, county of residence, calendar year, country of birth, educational attainment, number of healthcare visits, and cardiovascular-related comorbidities. Over a median of approximately 10 years of follow-up, 1,904 (7.6%) patients with CD, 4,154 (8.9%) patients with UC, and 990 (8.2%) patients with IBD-U developed arrhythmias, compared with 6.7%, 7.5%, and 6.0% in reference individuals, respectively. Compared with reference individuals, overall arrhythmias were increased in patients with CD [54.6 versus 46.1 per 10,000 person-years; aHR = 1.15 (95% CI [1.09, 1.21], P < 0.001)], patients with UC [64.7 versus 53.3 per 10,000 person-years; aHR = 1.14 (95% CI [1.10, 1.18], P < 0.001)], and patients with IBD-U [78.1 versus 53.5 per 10,000 person-years; aHR = 1.30 (95% CI [1.20, 1.41], P < 0.001)]. The increased risk persisted 25 years after diagnosis, corresponding to 1 extra arrhythmia case per 80 CD, 58 UC, and 29 IBD-U cases over the same period. Patients with IBD also had a significantly increased risk of specific arrhythmias, except for bradyarrhythmias. Sibling comparison analyses confirmed the main findings. Study limitations include lack of clinical data to define IBD activity, not considering the potential role of IBD medications and disease activity, and the potential residual confounding from unmeasured factors for arrhythmias.In this study, we observed that patients with IBD were at an increased risk of developing arrhythmias. The excess risk persisted even 25 years after IBD diagnosis. Our findings indicate a need for awareness of this excess risk among healthcare professionals.
Reply to Brusasco and Pellegrino
Authors: Kate M. A. Magner, Mathew Cherian, G. Alex Whitmore, Shawn D. Aaron
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Reply to: On the Assessment of Preserved Ratio Impaired Spirometry (PRISm)." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Exposure to polycyclic aromatic hydrocarbons, volatile organic compounds, and tobacco-specific nitrosamines and incidence of esophageal cancer
Authors: Arash Etemadi, Hossein Poustchi, Cindy M Chang, Antonia M Calafat, Benjamin C Blount, Deepak Bhandari, Lanqing Wang, Gholamreza Roshandel, Apostolos Alexandridis, Julianne Cook Botelho, Baoyun Xia, Yuesong Wang, Connie S Sosnoff, Jun Feng, Mahdi Nalini, Masoud Khoshnia, Akram Pourshams, Masoud Sotoudeh, Mitchell H Gail, Sanford M Dawsey, Farin Kamangar, Paolo Boffetta, Paul Brennan, Christian C Abnet, Reza Malekzadeh, Neal D Freedman
Journal: JNCI Journal of the National Cancer Institute (2023)

Studying carcinogens in tobacco and nontobacco sources may be key to understanding the pathogenesis and geographic distribution of esophageal cancer.
CD146 promotes malignant progression of breast phyllodes tumor through suppressing DCBLD2 degradation and activating the AKT pathway
Authors: Jiewen Chen, Qingji Xu, Dan Liu, Xun Li, Mingyan Guo, Xuehui Chen, Jianyou Liao, Rong Lei, Wende Li, Hongyan Huang, Phei Er Saw, Erwei Song, Xiyun Yan, Yan Nie
Journal: Cancer Communications (2023)

As a rapid-progressing tumor, breast malignant phyllodes tumors (PTs) are challenged by the lack of effective therapeutic strategies and suitable prognostic markers. This study aimed to clarify the role and mechanism of CD146 on promoting PTs malignant progression, and to identify a novel prognosis marker and treatment target of breast malignant PTs.The expression and prognostic significance of CD146 in PTs was detected through single-cell RNA-sequencing (scRNA-seq), immunostaining, real-time PCR and other methodologies. Functional experiments including proliferation assay, colony formation assay, transwell assay, and collagen contraction assay were conducted to validate the role of CD146 in malignant progression of PTs. The efficacy of anti-CD146 monoclonal antibody AA98 against malignant PTs was corroborated by a malignant PT organoid model and a PT patient-derived xenograft (PDX) model. Transcriptome sequencing, proteomic analysis, co-immunoprecipitation, and pull-down assay was employed to identify the modulating pathway and additional molecular mechanism.In this study, the scRNA-seq analysis of PTs disclosed a CD146-positive characteristic in the α-SMA+ fibroblast subset. Furthermore, a progressive elevation in the level of CD146 was observed with the malignant progression of PTs. More importantly, CD146 was found to serve as an independent predictor for recurrence in PT patients. Furthermore, CD146 was found to augment the viability and invasion of PTs. Mechanistically, CD146 acted as a protective "shield" to prevent the degradation of Discoidin, CUB, and LCCL domain-containing protein 2 (DCBLD2), thereby activating the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway and enhancing malignant behaviors of PT cells. In the malignant PT organoid and PDX model, a significant suppression of malignant PT growth was observed after the application of AA98.These findings suggested that CD146 served as an efficacious marker for predicting PT malignant progression and showed promise as a prognosis marker and treatment target of breast malignant PTs. The study further unveiled the essential role of the CD146-DCBLD2/PI3K/AKT axis in the malignant progression of PTs.
Depression and anxiety-related disorders and suicide among Swedish male elite football players: a nationwide cohort study
Authors: Manzur Kader, Björn Pasternak, Carl-Emil Lim, Martin Neovius, Magnus Forssblad, Henrik Svanström, Jonas F Ludvigsson, Peter Ueda
Journal: British Journal of Sports Medicine (2023)

Objective To assess whether male elite football players, during and after their active career, were at increased risk of depression and anxiety-related disorders and suicide, as compared with the general male population. Methods We included male football players active in the Swedish top division 1924–2019 and general male population (matched to football players based on age and region of residence) aged &lt;65 years in 1997. Using nationwide registers, we followed the football players from their first season in the top division (or the date of their first registered residency in Sweden) or 1 January 1997, and compared the risk of depression and anxiety-related disorders (captured through diagnoses from hospital admissions and outpatient visits, and use of prescription drugs) among football players versus controls. In a secondary analysis using data from death certificates, we compared the risk of suicide between football players and general population males who were alive in 1969 (when cause of death became available) . Results During follow-up through 31 December 2020, 504 (13.6%) of 3719 football players and 7455 (22.3%) of 33 425 general population males had a depression or anxiety-related disorder. In analyses accounting for age, region of residence and calendar time, the risk of anxiety and depression-related disorders was lower among football players versus general population males (HR 0.61, 95% CI 0.55 to 0.66). The protective association was attenuated with increasing age, and from around age 70 years the risk was similar in the two groups. The risk of suicide was lower among football players versus general population males (HR 0.48, 95% CI 0.32 to 0.72). Conclusions In this nationwide cohort study in Sweden, elite male football players had a lower risk of depression and anxiety-related disorders and suicide as compared with the general population.
Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases
Authors: Margaret G. Guo, David L. Reynolds, Cheen E. Ang, Yingfei Liu, Yang Zhao, Laura K. H. Donohue, Zurab Siprashvili, Xue Yang, Yongjin Yoo, Smarajit Mondal, Audrey Hong, Jessica Kain, Lindsey Meservey, Tania Fabo, Ibtihal Elfaki, Laura N. Kellman, Nathan S. Abell, Yash Pershad, Vafa Bayat, Payam Etminani, Mark Holodniy, Daniel H. Geschwind, Stephen B. Montgomery, Laramie E. Duncan, Alexander E. Urban, Russ B. Altman, Marius Wernig, Paul A. Khavari
Journal: Nature Genetics (2023)
AcSé-ESMART, a European precision cancer medicine proof-of-concept platform trial
Authors: Birgit Geoerger, Xavier Paoletti, Francisco Bautista, Susanne A. Gatz, Lynley V. Marshall, Nicolas André, Pablo Berlanga, Stephane Ducassou, Claudia Pasqualini, Michela Casanova, C. Michel Zwaan, Karsten Nysom, Jonathan Rubino, Delphine Vuillier-Le Goff, Baptiste Archambaud, Samuel Abbou, Gudrun Schleiermacher, Christelle Dufour, Patricia Blanc, Natalie Hoog-Labouret, Agnes Buzyn, Gilles Vassal
Journal: Nature Medicine (2023)
Proline uptake promotes activation of lymphoid tissue inducer cells to maintain gut homeostasis
Authors: Di Wu, Zongxian Li, Yime Zhang, Yinlian Zhang, Guanqun Ren, Yanyu Zeng, Huiying Liu, Weiqiang Guan, Xingyu Zhao, Peng Li, Luni Hu, Zhiyuan Hou, Jingjing Gong, Jun Li, Wenfei Jin, Zeping Hu, Changtao Jiang, Houhua Li, Chao Zhong
Journal: Nature Metabolism (2023)
Can salbutamol be used as a proxy for methacholine when assessing nebuliser performance for a methacholine challenge test?
Authors: Allan L. Coates, Myrtha Reyna-Vargas, Cathy C. Doyle, Mark W. Nagel
Journal: European Respiratory Journal (2023)

<h3>Tweetable abstract</h3> <b>There are differences between nebuliser outputs of methacholine and salbutamol, so caution is necessary if using salbutamol as a proxy for methacholine when determining device performance in order to calculate PD<sub>20</sub></b>https://bit.ly/3S47mnF
Organoid-guided synergistic treatment of minimal function CFTR mutations with CFTR modulators, roflumilast and simvastatin: a personalised approach
Authors: Sacha Spelier, Karin de Winter-de Groot, Natascha Keijzer-Nieuwenhuijze, Yves Liem, Kors van der Ent, Jeffrey Beekman, Lieke S. Kamphuis
Journal: European Respiratory Journal (2023)

Highly effective cystic fibrosis transmembrane conductance regulator (CFTR) protein-targeting modulator therapies (HEMTs) facilitate strong clinical improvements in a large proportion of people with CF (PwCF) [1, 2]. More specifically, the EMA and FDA approved combination of the CFTR modulators elexacaftor/tezacaftor/ivacaftor (ETI) for PwCF with at least one F508del allele, whilst the FDA extended eligibility for several rare genotypes [3, 4]. However, 10–15% of PwCF carry CFTR mutations that are unresponsive to HEMTs as monotherapy [1]. Furthermore, some pwCF suffer from HEMT intolerance or HEMTs are not accessible due to practical challenges such as lack of access due to high costs or legislation and approval challenges. Consequently, the focus in the CF research field has shifted towards filling the unmet clinical need for the PwCF that will not benefit from HEMTs. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article.
Mediators of the association between gastro-oesophageal reflux disease and idiopathic pulmonary fibrosis
Authors: Heqing Tao, Yongqiang Dong, Xueqing Chen, Liang Peng
Journal: European Respiratory Journal (2023)

The causal relationship between idiopathic pulmonary fibrosis (IPF) and gastroesophageal reflux disease (GERD) has long been a subject of debate. However, it was only in the last two months that two studies utilising Mendelian randomisation (MR) provided evidence of a significant causality between GERD and IPF, indicating that GERD indeed increases the risk of IPF. This finding has partially helped resolve the debate [1, 2]. Nevertheless, it should not be overlooked that previous meta-analyses have shown that treating GERD does not significantly improve the outcomes of IPF, contrary to expectations [3, 4]. This prompts us to consider the involvement of other intermediate variables, such as smoking, obesity, and telomere length, in the process of GERD-induced IPF [5]. In the present study, network MR will be employed to assess the potential mediating effect between GERD and IPF. This will help providing valuable insights into their underlying mechanisms and informing future therapeutic interventions. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article. Conflict of interest: The authors declare that they have no competing interests.